Combination of annotation methods

Working directory should contain root atlas Seurat object, which is available on GEO under record GSE152766:

Root_Atlas.rds (or get it by running through notebook 2, 3, 4, 5 & 6)

Working directory must contain subdirectories,supp_data

supp_data/ should contain the files, which are available on Github (github.com/Hsu-Che-Wei/COPILOT):

Protoplasting_DEgene_FC2_list.txt
cell_cycle_genes.csv
color_scheme_at.RData
Validated_Markers.csv
spatial_anno.txt (get it by running through notebook 3)
semitones.curated.marker.anno.nsds5.csv (get it by running through notebook 4)
semitones.curated.marker.csv (get it by running through notebook 4)
ici_raw_20200414.csv.bz2 (get it by running through notebook 5)

1. Load data

2. Z-Score annotation

3. SEMITONES (marker-based annotation)

4. Spatial mapping (novoSpaRc) annotation

5. Process ICI output

6. ICI annotation

7. Correlation-based annotation

8. Make consensus annotation

9. Build new reference expression profiles based on consensus annotation

Merge sub-types (crude annotation)